package phylogenetics

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Parameters
Signature

phylogenetics
- Phylogenetics
  - Alignment
    
    Fasta
    
    Make
    
    S
  - Alphabet
    
    Make
    
    Matrix
    
    Table
    
    Vector
    
    X
    
    S
    
    Matrix
    
    Table
    
    Vector
    
    S_int
    
    Matrix
    
    Table
    
    Vector
  - Amino_acid
    
    Matrix
    
    Table
    
    Vector
  - Birth_death
  - Bppsuite
    
    Cmd
  - Codon
    
    Genetic_code
    
    NS
    
    Matrix
    
    Table
    
    Vector
    
    Matrix
    
    S
    
    Matrix
    
    Table
    
    Vector
    
    Table
    
    Universal_genetic_code
    
    NS
    
    Matrix
    
    Table
    
    Vector
    
    Vector
  - Discrete_pd
  - Dna
  - Felsenstein
    
    Alignment
    
    Make
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    Align
    
    E
  - Fitch
  - ID_monad
  - Iupac_nucleotide
    
    Matrix
    
    Table
    
    Vector
  - Linear_algebra
    
    Matrix
    
    S
    
    Matrix
    
    Vector
    
    Vector
  - Linear_algebra_tools
    
    Lacaml
    
    Mat
    
    Vec
  - List1
  - MCMC
    
    M
    
    Alignment
    
    Felsenstein
  - Mutsel
    
    NSCodon_rate_matrix
  - Nelder_mead
  - Newick
    
    Tree_repr
  - Newick_ast
  - Newick_lexer
  - Newick_parser
    
    Incremental
    
    MenhirInterpreter
  - Newick_parser_errors
  - Nucleotide
    
    Matrix
    
    Table
    
    Vector
  - Nucleotide_process
    
    Random
  - Phylip
  - Phylo_ctmc
    
    Ambiguous
    
    Path_sampler
    
    Uniformized_process
  - Phylogenetic_tree
  - Rate_matrix
    
    Amino_acid
    
    Make
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    Nucleotide
    
    S
  - Rejection_sampling
    
    Make
    
    Align
  - Seq
    
    Base
    
    DNA
    
    Make
    
    B
    
    Make_list
    
    B
    
    S
  - Sequence_generation
    
    Base
    
    Make
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    Align
    
    E
    
    Seq
    
    Sequence
  - Sequence_simulator
    
    Alphabet
    
    Make
    
    A
  - Sigs
    
    ALIGNMENT
    
    BASE
    
    EVOL_MODEL
    
    SEQUENCE
  - Simulator
    
    Branch_info
    
    Make
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    BI
    
    NSCodon
    
    BI
  - Site_evolution_model
    
    Diagonalizable_rate_matrix
    
    JC69
    
    JC69_numerical
    
    K80
    
    K80_numerical
    
    Make
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    M
    
    Make_diag
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    M
    
    Nucleotide_S_with_reduction
    
    Rate_matrix
    
    S
    
    S_with_reduction
  - Stat_tools
  - TKF91
    
    Make_simulator
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    BI
  - Tree
  - Utils
  - Wag
  - Zipper

Legend:
Library
Module
Module type
Parameter
Class
Class type

Parameters

module BI : Branch_info

Signature

include sig ... end

val transition_matrix : 
  (BI.t -> Phylogenetics.Mutsel.NSCodon.matrix) ->
  BI.t ->
  Phylogenetics.Mutsel.NSCodon.matrix

val site_exponential_method : 
  Gsl.Rng.t ->
  ('n, 'l, BI.t) Tree.t ->
  root:Phylogenetics.Mutsel.NSCodon.t ->
  transition_matrix:(BI.t -> Phylogenetics.Mutsel.NSCodon.matrix) ->
  ('n * Phylogenetics.Mutsel.NSCodon.t,
    'l * Phylogenetics.Mutsel.NSCodon.t,
    BI.t)
    Tree.t

val branch_gillespie_direct : 
  Gsl.Rng.t ->
  start_state:Phylogenetics.Mutsel.NSCodon.t ->
  rate_matrix:Phylogenetics.Mutsel.NSCodon.matrix ->
  branch_length:float ->
  init:'a ->
  f:('a -> Phylogenetics.Mutsel.NSCodon.t -> float -> 'a) ->
  'a

val site_gillespie_direct : 
  Gsl.Rng.t ->
  ('n, 'l, BI.t) Tree.t ->
  root:Phylogenetics.Mutsel.NSCodon.t ->
  rate_matrix:(BI.t -> Phylogenetics.Mutsel.NSCodon.matrix) ->
  ('n * Phylogenetics.Mutsel.NSCodon.t,
    'l * Phylogenetics.Mutsel.NSCodon.t,
    BI.t)
    Tree.t

val site_gillespie_first_reaction : 
  Gsl.Rng.t ->
  ('n, 'l, BI.t) Tree.t ->
  root:Phylogenetics.Mutsel.NSCodon.t ->
  rate_matrix:(BI.t -> Phylogenetics.Mutsel.NSCodon.matrix) ->
  ('n * Phylogenetics.Mutsel.NSCodon.t,
    'l * Phylogenetics.Mutsel.NSCodon.t,
    BI.t)
    Tree.t

val sequence_gillespie_direct : 
  Gsl.Rng.t ->
  ('n, 'l, BI.t) Tree.t ->
  update_iterator:(n:int -> pos:int -> (int -> unit) -> unit) ->
  root:Phylogenetics.Mutsel.NSCodon.t array ->
  rate_vector:
    (BI.t ->
      Phylogenetics.Mutsel.NSCodon.t array ->
      int ->
      float Phylogenetics.Mutsel.NSCodon.table) ->
  ('n * Phylogenetics.Mutsel.NSCodon.t array,
    'l * Phylogenetics.Mutsel.NSCodon.t array,
    BI.t)
    Tree.t

val hmm0 : 
  Gsl.Rng.t ->
  len:int ->
  dist:(int -> float Phylogenetics.Mutsel.NSCodon.table) ->
  Phylogenetics.Mutsel.NSCodon.t array

val alignment : 
  Gsl.Rng.t ->
  (_, _, BI.t) Tree.t ->
  root:Phylogenetics.Mutsel.NSCodon.t array ->
  rate_matrix:(int -> BI.t -> Mutsel.NSCodon_rate_matrix.t) ->
  Dna.t list